9QI5 | pdb_00009qi5

Crystal structure of I105R mutant of BlaC from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.211 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A glycine at position 105 leads to clavulanic acid and avibactam resistance in class A beta-lactamases.

Radojkovic, M.Chikunova, A.Koene, S.F.Timmer, M.Natarajan, S.V.Boyle, A.L.Ubbink, M.

(2025) J Biological Chem : 110347-110347

  • DOI: https://doi.org/10.1016/j.jbc.2025.110347
  • Primary Citation of Related Structures:  
    9QI5, 9QI6, 9QI7

  • PubMed Abstract: 

    β-Lactamase enzymes exhibit extraordinary adaptive potential, thus rendering many β-lactam drugs ineffective. The residue at Ambler position 105, also known as the gatekeeper residue, plays an important role in substrate recognition, but its implication in inhibition mechanisms remains understudied and obscure. To inspect the relationship between inhibitor-resistant phenotypes and residues at this position, we performed site-saturation mutagenesis and extensive fitness profiling of five distinct class A β-lactamases using deep sequencing. We found that inhibitor resistance is readily detectable, with variants harboring Gly or Arg being the least susceptible to inhibitors. Mutation of Ile105 to Arg in the β-lactamase BlaC simultaneously enhances activity for carbenicillin and the ability to evade clavulanic acid inhibition. The Y105G substitution in two clinically important enzymes, CTX-M-14 and TEM-1, confers greatly reduced in vitro sensitivity to avibactam, which we attribute to elevated conformational flexibility of the inhibitor within the active site. The findings presented in this study underpin the gatekeeper residue as a possible mutational hotspot and might aid the design of novel β-lactamase inhibitors.


  • Organizational Affiliation

    Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
266Mycobacterium tuberculosisMutation(s): 1 
Gene Names: blaCblaABQ2027_MB2094C
EC: 3.5.2.6
UniProt
Find proteins for P0A5I7 (Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97))
Explore P0A5I7 
Go to UniProtKB:  P0A5I7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A5I7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.211 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.161α = 90
b = 40.975β = 90
c = 267.495γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)NetherlandsOCENW.KLEIN.264

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Database references